Shokor, F. | bioRxiv Science

bioRxiv2025

Trajectories of genetic correlations in populations under selection: from theory to a case-study

BackgroundBreeding programs select for multiple commercial traits, aiming to achieve genetic progress for all. Often, selection is based on a selection index, i.e. a linear combination of traits with weights defined by, among other information, the genetic correlation between traits. These correlations are typically estimated as a static parameter, and assumed equal to all individuals and generations. While research on the consequences of selection to genetic variances (Bulmer effect) is widely available, only a few studies focused on the consequences of selection to genetic correlations. Our study extended the already existing inferences about how selection affects genetic variances, to how multi-trait selection affects genetic correlations. In order to further our understanding of genetic correlations, we also proposed an alternative method to calculate genetic correlations between traits at the individual level, called by us as individualized sire genetic correlation (iSGC), obtained through the estimated breeding values (EBV) from evaluated daughters. Lastly, a case-study was performed on thirty years of data from the French Holstein dairy cattle population, for five traits studied pairwise: milk and protein yield, milking speed, somatic cell score, and cow conception rate. ResultsTheory revealed that multi-trait selection leads to an attenuation (decrease) of positive genetic correlations, with potential to revert them to negative values, if initially low. Uncorrelated traits will become negatively correlated, and negative genetic correlations will be either intensified or attenuated (decrease or increase, respectively), depending on selection intensity, weights applied to the selection index, and the initial genetic correlation. ConclusionBoth theory and empirical results on real data confirm that selection does change the genetic correlation between traits in a population under selection. Moreover, empirical trajectories of the iSGC were in better agreement with the theory, than trajectories of populational genetic correlations. The iSGC searches for individual-specific patterns of correlations, and since it is measured on sires through the EBV of their daughters, it also considers the recombination of the genetic background. Along with the fact that trajectories of iSGC were in better agreement with theory, we believe it to be a potentially less biased measure of genetic correlations between traits.

genetics↗

bioRxiv2024

Predicting nonlinear genetic relationships between traits in multi-trait evaluations by using a GBLUP-assisted Deep Learning model

BackgroundGenomic prediction aims to predict the breeding values of multiple complex traits, usually assumed to be normally distributed by the largely used statistical methods, thus imposing linear genetic correlations between traits. While statistical methods are of great value for genomic prediction, these methods do not account for nonlinear genetic relationships between traits. If such relationships exist, although statistical models do perform a fair linear approximation, their prediction accuracy is limited due to the nonlinearity. Deep learning (DL) is a promising methodology for predicting multiple complex traits, in scenarios where nonlinear genetic relationships are present, due to its capacity to capture complex and nonlinear patterns in large data. We proposed a novel hybrid DLGBLUP model which uses the output of the traditional GBLUP, and enhances its PGV by accounting for nonlinear genetic relationships between traits using DL. Using simulated data, we compared the accuracy of the PGV obtained with the proposed hybrid DLGBLUP model, a DL model, and the traditional GBLUP model - the latter being our baseline reference. ResultsWe found that both DL and DLGBLUP models either outperformed GBLUP, or presented equally accurate PGV, with a particular greater accuracy for traits presenting a strongly characterized nonlinear genetic relationship. Overall, DLGBLUP presented the highest prediction accuracy, up to 0.2 points higher than GBLUP, and smallest mean squared error of the PGV for all traits. Additionally, we evolved a base population over seven generations and compared the genetic progress when selecting individuals based on the additive PGV obtained by either DL, DLGBLUP or GBLUP. For all traits with a nonlinear genetic relationship, after the fourth generation, the observed genetic gain when selection was based on the additive PGV from GBLUP was always inferior to the one achieved from either DL or DLGBLUP. ConclusionsThe integration of DL into genomic prediction enables the possibility of modeling nonlinear relationships between traits. Moreover, by identifying these nonlinear genetic relationships, our DL and DLGBLUP models improved prediction accuracy, when compared to GBLUP. The possibility of nonlinear relationships between traits offers a different perspective into multi-trait evaluations and prediction, as well as into the traits evolution over generations, with potential to further improve selection strategies in commercial livestock breeding programs. Moreover, DLGBLUP shows that DL can be used as a complement to statistical methods, by enhancing their performance.

genomics↗